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Gigwa—Genotype investigator for genome-wide analyses

Sempere Guilhem, Philippe Florian, Dereeper Alexis, Ruiz Manuel, Sarah Gautier, Larmande Pierre. 2016. Gigwa—Genotype investigator for genome-wide analyses. GigaScience, 5 (25), 9 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Url - jeu de données : http://gigadb.org/dataset/100199

Quartile : Outlier, Sujet : MULTIDISCIPLINARY SCIENCES

Additional Information : Erratum paru dans GigaScience = ISSN 2047-217X. - (2016)vol.5:n°48 (1 p.)

Abstract : Background Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Description Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. Conclusions The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers. (Résumé d'auteur)

Mots-clés Agrovoc : Bioinformatique, Génome, Internet, Analyse de données, Banque de données, Variation génétique, Génie génétique, Application des ordinateurs

Mots-clés complémentaires : Séquencage

Classification Agris : C30 - Documentation and information
L10 - Animal genetics and breeding
F30 - Plant genetics and breeding
U10 - Mathematical and statistical methods

Champ stratégique Cirad : Hors axes (2014-2018)

Auteurs et affiliations

  • Sempere Guilhem, CIRAD-BIOS-UMR INTERTRYP (FRA)
  • Philippe Florian, IRD (FRA)
  • Dereeper Alexis, IRD (FRA)
  • Ruiz Manuel, CIRAD-BIOS-UMR AGAP (COL) ORCID: 0000-0001-8153-276X
  • Sarah Gautier, CIRAD-BIOS-UMR AGAP (FRA)
  • Larmande Pierre, IRD (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/580745/)

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